The genome sequence of the devil’s coach horse beetle, Ocypus olens (Müller, 1764)

We present a genome assembly from an individual female Ocypus olens (the devil’s coach horse; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence is 1,084 megabases in span. The majority (98.81%) of the assembly is scaffolded into 20 chromosomal pseudomolecules, with the X sex chromosome assembled.


Background
The devil's coach horse, Ocypus olens, is a large, all-black rove beetle.Reaching up to 32 mm, it is the largest beetle in the family Staphylinidae in the UK, and one of the largest worldwide.It is widespread and generally common across the Palaeartic including North Africa, including throughout mainland UK.It has been introduced to North America and Australasia.It can be found across a range of different habitats, especially damp woodland, grassland, brownfield sites and gardens.The devil's coach horse is largely nocturnal, sheltering under leaf litter, logs and stones during the day.It is a generalist predator as both a larva and adult, feeding on a wide range of invertebrate species and carrion (Bonacci et al., 2006).Adults can be found all year and overwintering occurs in this stage.Mating occurs in late summer/autumn and eggs are laid 2 to 3 weeks later (Nield, 1976).Adults can be relatively long-lived, living up to 2 years in this stage (Nield, 1976).When agitated, the abdomen is reared and the mandibles opened in a threat-posture.The devil's coach horse is capable of inflicting a painful bite to humans and readily produces defensive secretions from the mouth and tip of the abdomen.This species has been associated with evil and the devil in folklore since the Middle Ages.

Genome sequence report
The genome was sequenced from one female O. olens (Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.775, longitude -1.326).A total of 40-fold coverage in Pacific Biosciences single-molecule long reads and 41-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 541 missing/misjoins and removed 28 haplotypic duplications, reducing the assembly length by 0.45% and the scaffold number by 64.24%, and increasing the scaffold N50 by 188.60%.
The final assembly has a total length of 1,084 Mb in 188 sequence scaffolds with a scaffold N50 of 57.3 Mb (Table 1).The majority, 98.81%, of the assembly sequence was assigned to 20 chromosomal-level scaffolds, representing 19 autosomes (numbered by sequence length), and the X sex chromosome (Figure 2-Figure 5; Table 2).The order and orientation of scaffolds in the centromeric regions is less certain than in the rest of the assembly.The assembly has a BUSCO v5.1.2(Manni et al., 2021) completeness of 99.3% (single 98.2%, duplicated 1.1%) using the endopterygota_odb10 reference set.While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and nucleic acid extraction
A single female O. olens was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.775, longitude -1.326) by Liam Crowley, University of Oxford, using a pooter.The sample was identified by the same individual, snap-frozen on dry ice and stored using a CoolRack.
DNA was extracted from the whole organism of icOcyOlen1 at the Wellcome Sanger Institute (WSI) Scientific Operations core from the whole organism using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.Following this, further DNA was extracted for a PacBio top-up.Tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts.Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse.High molecular weight (HMW) DNA was again extracted using the Qiagen MagAttract HMW DNA extraction kit.HMW DNA was sheared into an average fragment size between 12-20 kb in a Megaruptor 3 system with speed setting 30.Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
RNA was extracted from the whole organism in the Tree of Life Laboratory at the WSI using TRIzol (Invitrogen), according to the manufacturer's instructions.RNA was then eluted in

Amendments from Version 1
The number of scaffolds and the number of autosomes have been corrected.The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016)   genome was analysed and BUSCO scores generated within the BlobToolKit environment (Challis et al., 2020).Table 3 contains a list of all software tool versions used, where appropriate.

Ethics/compliance issues
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The submission of materials by a Darwin Tree of Life Partner is subject to the  The genome Data Note for the devil's coach horse rove beetle presents a clear and comprehensive description of all the steps taken to generate the chromosomal-level assembly spanning just over 1 Gbp with almost 99% assigned to chromosomes including the X chromosome.As a species of ecological interest and as member of the largest order of insects, the rationale for generating these genomic resources is clear.The described data collection and analysis methods follow the best practices in the field and have delivered a high-quality complete and accurate chromosomelevel reference genome, with data made available through the European Nucleotide Archive.

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In the Hi-C contact map, is it only showing the 19 autosomes?

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Could there be an error in the total scaffold count, because the counts start at zero and go to 187, this means there are 188 scaffolds not 187 -please check.
○ "The genome will be annotated using the RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute."-it seems that this has now been done, so this statement could be updated in the revision.

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If it were made clear that 'icOcyOlen1' is the sample ID then the 'extracted from the whole organism of icOcyOlen1' sentence would make more sense.

Title:
There is no indication in the title that this is a beetle, or even an insect.Please consider revising the title to include the word "beetle" after the common name, and/or add ○ "(Coleoptera: Staphylinidae)" to the title in reference to the order and family of beetle sequenced.

Species Taxonomy:
Since you indicate both the author and year of publication for the name Ocypus olens, you should really include a citation to the original description.Alternatively, you could remove the year and only indicate the author last name.

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Line 5: Delete "and North Africa".By definition, North Africa is part of the Palaearctic.
○ Line 6: A citation is needed when referencing the introduced range.
○ Genome Sequence Report: Lines 2-3: The collection data appears in both this section and the Methods.This redundancy seems unnecessary.

Methods:
Line 1 in the second paragraph of the Methods: Delete "from the whole organism of icOcyOlen1."This is redundant with mention of extraction "from the whole organism" later in the same sentence.

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Was RNA extracted from the same "whole organism" as DNA?Please clarify.The same issue needs clarifying where "head tissue" is mentioned in reference to Hi-C data at the bottom of page 6.

Figure 1 .
Figure 1.Image of the icOcyOlen1 specimen taken prior to preservation and processing.

Figure 2 .
Figure 2. Genome assembly of Ocypus olens, icOcyOlen1.1:metrics.The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 1,083,870,412 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (69,741,075 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (57,303,393 and 48,121,331 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the endopterygota_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icOcyOlen1.1/dataset/CAJVAY01/snail.

Figure 3 .
Figure 3. Genome assembly of Ocypus olens, icOcyOlen1.1:GC coverage.BlobToolKit GC-coverage plot.Scaffolds are coloured by phylum.Circles are sized in proportion to scaffold length Histograms show the distribution of scaffold length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icOcyOlen1.1/dataset/CAJVAY01/blob.

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Figure 2 legend: 3 rd to last sentence: There is an excess period at the end of the sentence.○

Table 1 . Genome data for Ocypus olens, icOcyOlen1.1. Project accession data
(Guan et al., 2020).1%],F:0.2%,M:0.5%,n:2124*BUSCOscoresbased on the endopterygota_odb10 BUSCO set using v5.1.2.C= complete [S= single copy, D=duplicated], F=fragmented, M=missing, n=number of orthologues in comparison.A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.SequencingPacific Biosciences HiFi circular consensus and 10X Genomics Chromium read cloud sequencing libraries were constructed according to the manufacturers' instructions.Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit.Sequencing was performed by the ScientificGenome assemblyAssembly was carried out withHifiasm (Cheng et al., 2021); haplotypic duplication was identified and removed with purge_dups(Guan et al., 2020).One round of polishing was performed by aligning 10X Genomics read data to the assembly with longranger align, calling variants with freebayes

Table 3 . Software tools used.
The genome sequence is released openly for reuse.The O. olens genome sequencing initiative is part of the Darwin Tree of Life (DToL) project.All raw sequence data and the assembly have been deposited in INSDC databases.The genome will be annotated using the RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute.Raw data and assembly accession identifiers are reported in

the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed. ○Is

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
Reviewer Report 10 November 2021 https://doi.org/10.21956/wellcomeopenres.19172.r46916